opal

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Refactor SIMD code and add support for SSE2 and NEON

1

Hi from a Martin to another! I came to work on Opal since it's used in STAR, and I'm trying to improve the portability of some bioinformatics tools to new...

althonos

Hi, Below example that is causing segfault: ``` ./opal_aligner -o 1 -e 1 -x 2 -a NW -p test_query.fasta test_db.fasta -f test.mat ``` test_query.fasta: ``` >test query AABB ``` test_db.fasta:...

michal-kierzynka

no member named 'abs' in namespace 'std';

1

I got this error while trying to execute make > g++ -std=c++11 -march=native -Wall -O3 -c opal.cpp > opal.cpp:1169:45: error: no member named 'abs' in namespace 'std'; did you mean...

FadelBerakdar

Improve alignment speed

3

I should improve alignment speed. One thing I can do for sure is make alignment algorithm banded. I should also investigate if there are any other ways to make algorithm...

Martinsos

Information about E-value: http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=FAQ#expect . Implementation of E-value in SW#: http://sourceforge.net/p/swsharp/code/ci/master/tree/swsharp/src/evalue.cu .

Martinsos

Could I add SHW mode? Ivan Sovic said it would be useful.

Martinsos

Check this out and fix it, on match_bonus branch. I tried with gap open 0 and extend 1, with gap open 2 and gap extend 3, and I got errors...

Martinsos

Sometimes user may be confident that score will be in some range. In that case, I could allow him to specify for opal that overflow should not be checked. That...

Martinsos

Process multiple cells in one iteration, add padding to database sequences, optimize for cache

3

This method is explained in Rognes's article, under "Processing four consecutive cells along the database sequences". They claim that by processing multiple cells they have better usage of SSE registers...

Martinsos

made parameters as compatible as possible with NCBI Blast; fixes #6

2

fixing #6 and perform case insentive comparison of matrix names

tolot27